Mercurial > repos > recetox > msmetaenhancer

annotate msmetaenhancer_wrapper.py @ 8:2ada1099f42e draft

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planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
author recetox
date Thu, 18 May 2023 12:57:50 +0000
parents f387ebd6b734
children 791bf4d9b06c
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ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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1 import argparse
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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2 import asyncio
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3 import os
2ada1099f42e planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 538d6c063bb049fe7a08d7d4bd88af91c0d696e8
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4 import shutil
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5 import sys
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7 from matchms import set_matchms_logger_level
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8 from MSMetaEnhancer import Application
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11 def handle_xlsx_file(app, filename):
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12 basename = os.path.splitext(filename)[0]
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13 temp_file = basename + '.xlsx'
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14 app.save_data(temp_file, file_format='xlsx')
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15 shutil.copyfile(temp_file, filename)
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18 def main(argv):
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19 parser = argparse.ArgumentParser(description="Annotate spectra file.")
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20 parser.add_argument("--input_file", type=str, help="Path to query spectra file.")
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21 parser.add_argument("--file_format", type=str, help="Format of the input and the output files.")
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22 parser.add_argument("--output_file", type=str, help="Path to output spectra file.")
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23 parser.add_argument("--jobs", type=str, help="Sequence of conversion jobs to be used.")
ce612a11b455 "planemo upload for repository https://github.com/RECETOX/galaxytools/tree/master/tools/msmetaenhancer commit 26bede767f65ec97ac84b8cc3309db0aced22d53"
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24 parser.add_argument("--log_file", type=str, help="Path to log with details of the annotation process.")
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25 parser.add_argument("--log_level", type=str, default='info',
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26 help="Severity of log messages present in the log file.")
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27 args = parser.parse_args()
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29 app = Application(log_level=args.log_level, log_file=args.log_file)
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31 # set matchms logging level to avoid extensive messages in stdout while reading file
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32 set_matchms_logger_level("ERROR")
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33 # import spectra file
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34 app.load_data(args.input_file, file_format=args.file_format)
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36 # set matchms logging level back to warning
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37 set_matchms_logger_level("WARNING")
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39 # curate given metadata
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40 app.curate_metadata()
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42 # specify requested services and jobs
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43 services = ['PubChem', 'CTS', 'CIR', 'RDKit', 'IDSM', 'BridgeDb']
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45 if len(args.jobs) != 0:
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46 jobs = []
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47 for job in args.jobs.split(","):
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48 if len(job) != 0:
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49 jobs.append(job.split())
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50 asyncio.run(app.annotate_spectra(services, jobs))
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51 else:
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52 # execute without jobs parameter to run all possible jobs
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53 asyncio.run(app.annotate_spectra(services))
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54
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55 # export spectra file
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56 if args.file_format == 'xlsx':
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57 handle_xlsx_file(app, args.output_file)
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58 else:
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59 app.save_data(args.output_file, file_format=args.file_format)
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60 return 0
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63 if __name__ == "__main__":
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64 main(argv=sys.argv[1:])